The Chemical Level of Organization Notes PDF

The Chemical Level of Organization BIOL 1190: Ch 2 – Dr. Katelyn Janzen Outline  Basic chemistry – Self-review (notes posted on Brightspace)  How matter is organized (2.1)  Chemical bonds (2.2)  The water molecule (2.4)  Chemical reactions (2.3)  Organic Compounds (2.5-2.9)  Ene...

The Chemical Level of Organization BIOL 1190: Ch 2 – Dr. Katelyn Janzen Outline  Basic chemistry – Self-review (notes posted on Brightspace)  How matter is organized (2.1)  Chemical bonds (2.2)  The water molecule (2.4)  Chemical reactions (2.3)  Organic Compounds (2.5-2.9)  Energy currency: ATP (2.10) Learning Outcomes  Describe how matter is organized (2.1)  Explain how chemical bonds form and distinguish between the different types of bonds (2.2)  Describe the properties of the water molecule and explain why water is ‘the solvent of life’ (2.4)  Understand the pH scale and how buffers work (2.4)  Describe how chemical reactions occur and the function of catalysts (2.3)  List the groups of organic molecules, and define and provide examples of monomers and polymers (for those that form polymers) (2.5)  Carbohydrates: describe the structure and explain the primary function (2.6)  Lipids: describe the form and function of the three main lipid types (2.7)  Proteins: explain how amino acid structure contributes to protein structure, and how denaturation affects proteins (2.8)  DNA/RNA: identify the differences between DNA and RNA in structure and function (2.9)  Explain how ATP is used in the human body (2.10)  Organic Compouonds 4 major classes of Macromolecules: Carbohydrates Proteins Lipids Nucleic Acids Organic Compounds  Almost all molecules made by cells are composed of __________bonded to one another and to atoms of other elements (especially H, O, N)  Carbon is unparalleled in its ability to form large, diverse molecules  Compounds synthesized by cells and containing carbon are known as ______________  An organic compound must contain one or more C atoms covalently bonded to atoms of other elements (H, O, or N most commonly)  Proteins, DNA, carbohydrates, and other molecules that characterize living matter are all composed of carbon compounds How many bonds can each carbon atom form? This allows for great diversity of molecules and forms the basis for all life on Earth! Large Biological molecules  Large ________________ may be composed of thousands of atoms  The four major classes of large biological macromolecules are:  Carbohydrates  Nucleic acids  Proteins  Lipids  Macromolecules are made by __________________covalently bonded together to form large molecules  Cells make large molecules by joining small organic molecules together into chains called polymers  Polymer = large molecule consisting of many identical or similar _____________strung together  Monomer = units that serve as the building blocks of polymers Polypeptide chain Nucleic acid strand polymerization Carbohydrate string Covalent bonds  Making and Breaking Polymers Cells link monomers together to Cells break polymers down to form polymers by monomers by __________ _______________________ reactions  Carbohydrates  Provide _______ to cells  Are the source of must of the chemical energy needed to generate ATP  3 different types (based on length)  Monosaccharides  Simplest form  E.g., Glucose  _______________  Two monosaccharides together  E.g., sucrose = glucose + fructose  Polysaccharides  ___________of monosaccharides  E.g. starch, glycogen Glycogen Synthesis of carbohydrates  Carbohydrates Contain many –OH groups H C O Are carbohydrates non-polar or H C OH polar? HO C H H C OH Are carbohydrates hydrophilic or H C OH hydrophobic? CH2OH  Polysaccharides  _____________  Energy storage polysaccharide of animals  Humans and other vertebrate store glycogen mainly in the liver and skeletal muscles  Consists of glucose monomers  Starch  Energy storage polysaccharide of _______  Consists of glucose monomers (identical to starch but less compact; unbranched)  Cellulose  Structural polysaccharide in plants; main component of plant cell walls  Also made of glucose, but linked differently than starch and glycogen  Most abundant organic material on earth Why does lettuce have less calories for humans than potatoes? Examples of Polysaccharides Lipids  Lipids are ________________that are grouped together because they share one trait: They do not mix well with water because they are hydrophobic  What makes them hydrophobic?  Why are hydrocarbons hydrophobic?  The most biologically relevant lipids are triglycerides, phospholipids, and steroids  Lipids are NOT formed of monomers linked together Triglycerides  Made from 2 kinds of smaller molecules  1 x glycerol backbone  3 x fatty acids  Main function of triglycerides is _________________  Another name for triglycerides is fats  Fatty acids are attached to glycerol by dehydration synthesis Triglycerides  The identity of a specific triglyceride is dependent on the type of fatty acids it contains  Fatty acids vary in length (number of C atoms) and in the number and locations of double bonds Unsaturated vs Saturated Fatty acids  ___________________have the maximum number of hydrogen atoms possible and no double bonds  _______ at room temperature  Mainly derived from animals  ___________fatty acids have one or more double bonds  _________ at room temperature  Mainly derived from plants (cis fatty acids)  Can contain cis or trans double bonds  Trans fatty acids are mostly produced  Increase LDL (bad) cholesterol and decrease (HDL (good) cholesterol, increase the risk of heart disease  Phospholipids  Phospholipids are similar to fats, but contain a phosphate group  Are ____________ – having both hydrophilic and hydrophobic regions  Forms bilayers  The basis of cellular membranes! Steroids  Steroids are lipids with carbon skeletons bent to form 4 fused rings  All steroids are made from ____________ (a four ringed structure) as a starting molecule  Steroid examples: some vitamins, bile salts, some hormones  Cholesterol serves as an important component of cell membranes and as ________________ for synthesizing other steroids Steroids in the membrane Proteins  Proteins give structure to the body, regulate processes, provide protection, help muscles contract, transport substances, and serve as Structural enzymes  Nearly every dynamic function in your body depends on proteins Catalytic Regulatory  Proteins DO THINGS!!! Proteins  Proteins are the most diverse class of macromolecules Transport Contractile  Contain: Carbon, hydrogen, ________, and __________ Immunological Proteins are amino acids linked together  The monomers of proteins are ______________  There are 20 different amino acids  All have the same general structure but different R groups Proteins are amino acids linked together  Protein structure determines its function  Different proteins vary in __________ and in the __________ of amino acids  Amino acids are linked together by dehydration synthesis  Different combinations of the 20 amino acids results in different proteins  Proteins are on average 300 a.a. long, but can be formed for as few as 10 a.a, and up to 2000 a.a.  The four levels of protein structure  _________ structure:  Linear sequence of amino acids  _____________ structure  α-helix and β-sheets formed by hydrogen bonds between atoms of the polypeptide backbone  __________structure  3-D structure formed by interactions between R groups  ___________ structure  Association of multiple polypeptides Bonds of Tertiary and Quaternary Structure  The sequence of amino acids determines the protein’s structure  The shape (structure) of the protein determines its function Changes to protein structure impacts protein function  In addition to the sequence of amino acids, _____________________________can affect protein structure  Alterations in pH, salt concentrations, temperature, other environmental factors  Loss of a protein’s structure native structure is called ____________  Denatured proteins can no longer perform their function = biologically inactive  All proteins can be denatured, but not all proteins can be renatured Protein denaturation Enzymes  Enzymes are proteins that act as biological catalysts  Recall: What is a catalyst?  Enzymes speed up the rate of reactions by ________ the amount of activation energy required to ______ the reaction  Enzymes are not consumed or changed during the reaction  Can be used over and over  Enzymes do not make non-spontaneous reactions ______________, but rather speed up spontaneous reactions  E.g., lighting sugar on fire A specific enzyme catalyzes each cellular reaction  Enzymes are _________  Selectivity determines which chemical reactions can or cannot occur in a cell  Specificity is due to the shape of the enzyme  I.e., Lock and key  Substrate: the specific reactant on which the enzyme acts  Active site: the site on an enzyme to which the substrate binds E.g. Digestive enzyme in action Nucleic Acids: DNA and RNA  Nucleic acids are macromolecules that ______ information required to build proteins Nucleic acids Nucleotides  Nucleic acids = __________  Nucleotides are the monomers that make up nucleic acids  Nucleotides all have the same general structure  All have _________ group, ___________ sugar, and nitrogenous base Synthesis of Polynucleotides  Nucleotides are joined by dehydration synthesis to form polynucleotide chains DEHYDRATION SYNTHESIS  Nucleotides  DNA pentose sugar is  RNA pentose sugar is ribose deoxyribose  Ribonucleic acid  Deoxyribonucleic acid  DNA is made up of 4 different  RNA is made up of 4 different types of nucleotides types of nucleotides  Adenine (A)  Adenine (A)  Thymine (T)  ____________instead of Thymine  Cytosine (C)  Cytosine (C)  Guanine (G)  Guanine (G) RNA  Usually consists of a single polynucleotide strand  _______________________________ causes it to fold into a 3D shape  3 main types of RNA  mRNA (messenger)  rRNA (ribosomal)  tRNA (transfer) DNA  DNA is formed of two strands that come together to form ________________  The two strands are held together by hydrogen bonds according to the following base pairing rules  A pairs with T  C pairs with G Energy Currency: ATP  Recall: Chemical Reactions and Energy  Catabolic pathways ________________by breaking down complex molecules in simpler compounds  “Exergonic” = release energy  Anabolic pathways _____________ to build complex molecules from simpler ones  “Endergonic” = requires energy ATP is used to couple reactions together  Anabolic and catabolic reactions are coupled together by ATP  The energy released from exergonic reaction are used to drive endergonic reactions = __________________  Most energy coupling in cells is mediated by ATP (adenosine triphosphate) What type of molecule is ATP? ATP powers cellular work  ATP powers cellular work through ________________  Transfer of a phosphate group  When ATP is ___________ it phosphorylates the reactant and energy is released  ATP is used to drive almost all endergonic reactions in the cell The ATP cycle  ATP is a ___________________  When exergonic reactions release energy, that energy is stored in ATP molecules  Potential energy stored in food molecules is released by the process of cellular respiration and used to synthesize ATP  Then ATP is used to power endergonic reactions  Review: Macromolecules Class of Monomers Polymers Elements Functions Macromolecule Carbohydrates Lipids Proteins Nucleic Acids